I assuming you are profiling IIS rather than Silverlight? (I guess so, as SL 3 doesn’t support profiling).
In that case, the solution is easy: minimize the 64-bit IE that ANTS launches and launch your own copy of the 32-bit IE: you can just paste the URL from the 64-bit version. The IE window we pop up is only used to manage the session and show that profiling is happening.
We will be adding functionality in future builds to specify the browser that's used.